Antigen-specific T lymphocyte signaling occurs through clonally distributed receptors (TCR), regulating thymocyte selection and peripheral effector responses, but the quantitative and qualitative relationships between receptor occupancy and this signaling remain poorly understood. This project uses cellular, biochemical, and molecular approaches to study differentiation of thymocytes and activation of T cells upon TCR-ligand interaction. We have re-analyzed the transition of CD4+CD8+ thymocytes to CD4+ and CD8+ mature cells and discovered that previously proposed models for this process, including our own, are flawed. Our new results indicate a complex pattern to coreceptor expression changes following MHC-dependent TCR signaling, leading to transitional phenotypes not expected by assuming linear CD4 or CD8 expression extinction upon initiation of selection. These new data explain previous discrepancies in the literature concerning this differentiation process and are leading to new insights into the sequential signals involved in thymocyte positive selection and lineage commitment. Characterization of mature and transitional phenotype cells in invariant chain-deficient mice has also allowed new insights into the quantitative parameters of thymocyte deletion. We previously reported that some TCR ligands evoke only a subset of CD4+ T cell effector responses or antagonize cytokine production induced by receptor agonists, and that such variant ligands induce only a subset of the tyrosine phosphorylation events typically accompaning agonist recognition. We have now extended these observations to CD8+ T cells, explored how such altered signaling affects biological responses such an anergy and cell death, and demonstrated that disturbed signaling can also arise from alterations in a cells' capacity to recruit molecules such as CD4 into forming signaling complexes. Along with our work on the molecular organization of signal transduction complexes (Z01 AI 00349-13 LI), this helps explain how protein-protein interactions result in antigen receptor-dependent second messenger generation and how specific intracellular signals contribute to the downstream gene activation events in T cells that control effector function, tolerance induction, and cell death.